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lfcThreshold
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4
replies
2.1k
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DESeq2 lfcThreshold - all my padj are equal to 1
DESeq2
lfcThreshold
2.5 years ago
Abir.khazaal
▴ 10
1
vote
2
replies
2.6k
views
DEseq2 anlysis - LfcThreshold and Lfcshrink options
lfcshrink
DESeq2
RNASeq
lfcthreshold
2.6 years ago
ClaudiaE
• 0
0
votes
5
replies
2.6k
views
Deseq2, lfcThreshold .
ashr
Deseq2
lfcThreshold
updated 3.4 years ago by
Michael Love
43k • written 4.9 years ago by
Iryna
• 0
27
votes
17
replies
8.8k
views
DESeq2 1.20.0 lfcshrink function
deseq2
differential expression
logfoldchange
lfcshrink
lfcthreshold
updated 3.8 years ago by
Michael Love
43k • written 6.7 years ago by
emi.sch
▴ 50
0
votes
1
reply
1.3k
views
DESeq2 - shrunken log fold changes and threshold test
deseq2
lfcshrink
lfcthreshold
differential gene expression
updated 6.3 years ago by
Michael Love
43k • written 6.3 years ago by
corentinrichard374369
• 0
1
vote
2
replies
2.7k
views
[DESeq2] Results summary indicates LFC > and < 0 even with changed lfcThreshold
DESeq2
lfcThreshold
updated 7.0 years ago by
Michael Love
43k • written 7.0 years ago by
Mike
▴ 10
9
votes
2
replies
6.2k
views
log fold change threshold in Deseq2 - using lfcthreshold
lfcthreshold
deseq2
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
lirongrossmann
▴ 80
2
votes
1
reply
3.4k
views
Setting a good lfcThreshold-value in DESeq2 to find stably expressed microRNAs
deseq2
microrna
lfcThreshold
stable expression
ffpe
updated 9.4 years ago by
Michael Love
43k • written 9.4 years ago by
mariakarand
▴ 20
8 results • Page
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Comment: how many significant figures are there in DESeq2 output
by
ATpoint
★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression
by
Jane
• 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga
by
Jane
• 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output
by
Matthew McCormack
▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to
by
ATpoint
★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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